Another question: Some of the outputs don't have the strain name. I guess the reason is that the organism name doesn't have that info. For example here https://www.ncbi.nlm.nih.gov/assembly/GCF_003290365.1/. If I use
for f in GCF* ; do term=$(echo $f | cut -f1,2 -d'_') ; esearch -db assembly -q $term | esummary | xtract -pattern DocumentSummary -sep ' ' -element Organism,Strain,AssemblyAccession | sed 's/ /_/g' ; done > filenames.txt
The strain name doesn't appear on filenames.txt. Could you please let me know what I'm doing wrong?